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diff --git a/docs/news/index.html b/docs/news/index.html index df6d53db..f8504768 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -122,22 +122,22 @@ </div> - <div id="mkin-0-9-49-5-2019-06-04" class="section level1"> + <div id="mkin-0-9-49-5-2019-07-03" class="section level1"> <h1 class="page-header"> -<a href="#mkin-0-9-49-5-2019-06-04" class="anchor"></a>mkin 0.9.49.5 (2019-06-04)<small> Unreleased </small> +<a href="#mkin-0-9-49-5-2019-07-03" class="anchor"></a>mkin 0.9.49.5 (2019-07-03)<small> Unreleased </small> </h1> <ul> -<li><p>Several algorithms for minimization of the negative log-likelihood for non-constant error models (two-component and variance by variable). In the case the error model is constant variance, least squares is used as this is more stable. The default algorithm tries direct minimization and a three step procedure, and returns the model with the highest likelihood.</p></li> +<li><p>Several algorithms for minimization of the negative log-likelihood for non-constant error models (two-component and variance by variable). In the case the error model is constant variance, least squares is used as this is more stable. The default algorithm ‘d_3’ tries direct minimization and a three-step procedure, and returns the model with the highest likelihood.</p></li> <li><p>The argument ‘reweight.method’ to mkinfit and mmkin is now obsolete, use ‘error_model’ and ‘error_model_algorithm’ instead</p></li> <li><p>Add a test that checks if we get the best known AIC for parent only fits to 12 test datasets. Add these test datasets for this purpose.</p></li> <li><p>New function ‘mkinerrplot’. This function is also used for residual plots in ‘plot.mmkin’ if the argument ‘resplot = “errmod”’ is given, and in ‘plot.mkinfit’ if ‘show_errplot’ is set to TRUE.</p></li> -<li><p>Remove dependency on FME, only use nlminb for optimisation</p></li> -<li><p>Use the numDeriv package to calculate hessians</p></li> -<li><p>Add a benchmark vignette to document the impact on performance. For very simple fits, the new code is a bit slower, presumably because of the time it takes to calculate the hessian matrices with and without parameter transformation</p></li> -<li><p>The code for manual weighting was removed</p></li> -<li><p>The fitting time reported in the summary now includes the calculation of the hessians</p></li> +<li><p>Remove dependency on FME, only use nlminb for optimisation (‘Port’ algorithm). I cannot remember cases where one of the other optimisation algorithms was preferable, except that I sometime used Levenberg-Marquardt for speed in cases where I did not expect to get trapped in a local minimum.</p></li> +<li><p>Use the numDeriv package to calculate hessians. This results in slightly different confidence intervals, takes a bit longer, but is apparently more robust</p></li> +<li><p>Add a simple benchmark vignette to document the impact on performance.</p></li> +<li><p>The code for manual weighting was removed. This functionality might get added again at a later time.</p></li> +<li><p>The fitting time reported in the summary now includes the time used for calculation of the hessians</p></li> <li><p>Adapt tests</p></li> -<li><p>Fix an error in the FOCUS chi2 error level calculations that occurred if parameters were specified in parms.ini that were not in the model. A warning was already issued, but when fitting via mmkin this could easily go unnoticed.</p></li> +<li><p>Fix an error in the FOCUS chi2 error level calculations that occurred if parameters were specified in parms.ini that were not in the model. A warning was already issued, but when fitting in parallel via mmkin this could go unnoticed.</p></li> </ul> </div> <div id="mkin-0-9-48-1-2019-03-04" class="section level1"> @@ -698,7 +698,7 @@ <div id="tocnav"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#mkin-0-9-49-5-2019-06-04">0.9.49.5</a></li> + <li><a href="#mkin-0-9-49-5-2019-07-03">0.9.49.5</a></li> <li><a href="#mkin-0-9-48-1-2019-03-04">0.9.48.1</a></li> <li><a href="#mkin-0-9-47-5-2018-09-14">0.9.47.5</a></li> <li><a href="#mkin-0-9-47-3">0.9.47.3</a></li> |